[med-svn] [Git][med-team/ncbi-blastplus][master] 19 commits: New upstream version 2.15.0+ds

[Aaron M. Ucko (@ucko)]

Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus


Commits:
67807fe0 by Aaron M. Ucko at 2024-07-17T21:22:59-04:00
New upstream version 2.15.0+ds
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fbfbf2ee by Aaron M. Ucko at 2024-07-17T21:28:39-04:00
Merge tag 'upstream/2.15.0+ds' (#1074316).

Upstream version 2.15.0(+ds) should be (more than) new enough for
recent q2-feature-classifier, which merely needs at least 2.13.

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abe67c72 by Aaron M. Ucko at 2024-07-17T21:39:29-04:00
d/patches: Update for new release (2.15.0[+ds]), mostly formally.

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c492f265 by Aaron M. Ucko at 2024-07-22T23:20:45-04:00
BDA on libnghttp2-dev, libsqlite3-dev, and libuv1-dev, newly needed.

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135c5cbd by Aaron M. Ucko at 2024-07-22T23:29:52-04:00
Move debian/patches/system_mbedtls_only up and extend it.

* debian/patches/series: Move system_mbedtls_only up in conjunction
  with incorporating part of an upstream patch needed by
  support_mbedtls3.
* debian/patches/system_mbedtls: Extend to cover ncbi_mbedtls.c (as in
  https://github.com/ncbi/ncbi-cxx-toolkit-public/commit/f9c7297dd1)
  and Makefile.xxconnect2.lib.

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a3d3e495 by Aaron M. Ucko at 2024-07-22T23:30:47-04:00
d/p/support_mbedtls3 (new): Support Mbed TLS 3.x (#1075867).

Don't specifically require it, though.

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f9d97278 by Aaron M. Ucko at 2024-07-22T23:30:56-04:00
Regenerate configure and config.h.in with Autoconf 2.69.

To that end, add a B-D on autoconf2.69.

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bdc3fc7f by Aaron M. Ucko at 2024-07-22T23:31:22-04:00
Make it possible to build against PCRE2, and do so (#891197).

* debian/control: Build against libpcre2-dev.
* debian/patches/allow_pcre2 (new): Allow use of PCRE2.
* debian/rules: Build against PCRE2.

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8f6aa0b1 by Aaron M. Ucko at 2024-07-22T23:31:32-04:00
Refresh patches after prepending allow_pcre2 and support_mbedtls3.

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ad520e4e by Aaron M. Ucko at 2024-07-22T23:31:32-04:00
debian/rules: Add --without-strip, disable reproducible=timeless.

Tune flags: Add --without-strip to make --with-symbols effective;
switch off warnings from __DATE__/__TIME__ usage, since
dpkg-buildpackage's SOURCE_DATE_EPOCH injection should suffice.

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e016e597 by Aaron M. Ucko at 2024-07-22T23:32:00-04:00
debian/patches/series: Comment out reprobuild (overkill).

I'm all for reproducibility, but the package already automatically
builds with flags that make __FILE__ relative, and many of its uses
are in header-defined macros that intend to pick up their callers'
paths.

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a1513d3e by Aaron M. Ucko at 2024-07-22T23:32:03-04:00
debian/rules: Extend generated-sources cleanup to objtools/eutils.

Not entirely straightforward due to input format variation.

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6bdc2344 by Aaron M. Ucko at 2024-07-22T23:32:03-04:00
debian/source/lintian-overrides: No more rapidjson10 (just ...11).

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a9e68c34 by Aaron M. Ucko at 2024-07-25T20:00:49-04:00
Stop relying on 2to3 at build time.

* debian/control: Stop building against 2to3, which may not be around
  much longer.
* debian/patches/allow_pcre2 (new): Allow use of PCRE2.
* debian/rules: Drop build-time 2to3 invocation in favor of
  debian/patches/2to3.

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e69e9a2f by Aaron M. Ucko at 2024-07-25T20:02:52-04:00
New upstream version 2.16.0+ds
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e5d75ace by Aaron M. Ucko at 2024-07-25T20:40:28-04:00
Merge tag 'upstream/2.16.0+ds'

Upstream version 2.16.0(+ds).

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4678cd3f by Aaron M. Ucko at 2024-07-25T20:41:04-04:00
routine-update: Standards-Version: 4.7.0

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19a32770 by Aaron M. Ucko at 2024-07-25T20:41:15-04:00
Update patches again for 2.16.0(+ds).

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1411bc81 by Aaron M. Ucko at 2024-07-25T20:41:31-04:00
Finalize ncbi-blast+ 2.16.0+ds-1 for unstable.

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30 changed files:

- c++/compilers/cygwin/build.sh
- c++/compilers/unix/GCC.sh
- c++/compilers/unix/ICC.sh
- c++/compilers/unix/Xcode.sh
- − c++/compilers/vs2017/Makefile.WinMain.app.msvc
- − c++/compilers/vs2017/Makefile.wxWidgets.app.msvc
- − c++/compilers/vs2017/build.sh
- − c++/compilers/vs2017/build_exec.bat
- − c++/compilers/vs2017/build_util.sh
- − c++/compilers/vs2017/check.sh
- − c++/compilers/vs2017/configure.bat
- − c++/compilers/vs2017/datatool.bat
- − c++/compilers/vs2017/dll/build/UtilityProjects/_CONFIGURE_.vcxproj
- − c++/compilers/vs2017/dll/build/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj
- − c++/compilers/vs2017/dll/build/UtilityProjects/configure._
- − c++/compilers/vs2017/dll/build/UtilityProjects/configure_dialog._
- − c++/compilers/vs2017/dll/build/all.bat
- − c++/compilers/vs2017/dll/build/all_gbench.bat
- − c++/compilers/vs2017/dll/build/all_gui.bat
- − c++/compilers/vs2017/dll/build/all_ncbi.bat
- − c++/compilers/vs2017/dll/build/gbench/UtilityProjects/_CONFIGURE_.vcxproj
- − c++/compilers/vs2017/dll/build/gbench/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj
- − c++/compilers/vs2017/dll/build/gbench/UtilityProjects/configure._
- − c++/compilers/vs2017/dll/build/gbench/UtilityProjects/configure_dialog._
- − c++/compilers/vs2017/dll/build/gbench/configure_prebuild.bat
- − c++/compilers/vs2017/dll/build/gbench/gbench_install/gbench-install.vcxproj
- − c++/compilers/vs2017/dll/build/gbench/ncbi_gbench.sln
- − c++/compilers/vs2017/dll/build/gui/UtilityProjects/_CONFIGURE_.vcxproj
- − c++/compilers/vs2017/dll/build/gui/UtilityProjects/_CONFIGURE_DIALOG_.vcxproj
- − c++/compilers/vs2017/dll/build/gui/UtilityProjects/configure._


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View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/77519daef0c13c73c6ad8b1d9a4a7dfe48cc97d1...1411bc81806aad716ae2e204821a73378587bf88

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